From 80774eed9a0d2e8f7dc884819b3270e928dce46c Mon Sep 17 00:00:00 2001
From: pavlemarinkovic <pavle.marinkovic@sbgenomics.com>
Date: Mon, 24 Jun 2024 16:14:46 +0200
Subject: [PATCH 1/4] NF schema is built only if it's missing Use wrabbit 0.2.0

---
 requirements.txt          | 2 +-
 sbpack/noncwl/manifest.py | 4 +++-
 sbpack/noncwl/nextflow.py | 2 ++
 sbpack/version.py         | 2 +-
 4 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index 268ee49..cb076c3 100755
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,6 +1,6 @@
 ruamel.yaml >= 0.16
 sevenbridges-python >= 2.0
 nf-core==2.1
-wrabbit==0.1.3
+wrabbit==0.2.0
 cwlformat
 packaging
\ No newline at end of file
diff --git a/sbpack/noncwl/manifest.py b/sbpack/noncwl/manifest.py
index 3dd1a96..cb87120 100755
--- a/sbpack/noncwl/manifest.py
+++ b/sbpack/noncwl/manifest.py
@@ -134,6 +134,8 @@ def validate_sheet(
             continue
         else:
             basename = os.path.basename(path)
+            if not basename:
+                continue
             parent = None
             if os.path.dirname(path):
                 parent = checked[os.path.dirname(path)]
@@ -239,7 +241,7 @@ def main():
         help="Name of the output file.",
     )
     parser.add_argument(
-        "--upload", '-u', action='store_true', required=False,
+        "--upload", action='store_true', required=False,
         help="Upload the file to the project after making it.",
     )
     parser.add_argument(
diff --git a/sbpack/noncwl/nextflow.py b/sbpack/noncwl/nextflow.py
index 84ec02c..f52950b 100755
--- a/sbpack/noncwl/nextflow.py
+++ b/sbpack/noncwl/nextflow.py
@@ -252,6 +252,8 @@ def main():
         # Do this only if the nextflow_schema.json is missing
         if not nf_wrapper.nf_schema_path:
             nf_wrapper.nf_schema_build()
+            # update the nextflow_schema.json location
+            nf_wrapper.init_config_files()
 
         # Create app
         nf_wrapper.generate_sb_app(
diff --git a/sbpack/version.py b/sbpack/version.py
index 6588dfc..abb3831 100755
--- a/sbpack/version.py
+++ b/sbpack/version.py
@@ -1 +1 @@
-__version__ = "2024.6.3rc1"
+__version__ = "2024.6.24rc1"

From ae2df4847bc933b236920474a15f9994ea75886e Mon Sep 17 00:00:00 2001
From: pavlemarinkovic <pavle.marinkovic@sbgenomics.com>
Date: Thu, 11 Jul 2024 17:22:06 +0200
Subject: [PATCH 2/4] Use wrabbit 0.2.1

---
 requirements.txt          |  2 +-
 sbpack/noncwl/nextflow.py | 12 +++++-------
 2 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index cb076c3..69b3136 100755
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,6 +1,6 @@
 ruamel.yaml >= 0.16
 sevenbridges-python >= 2.0
 nf-core==2.1
-wrabbit==0.2.0
+wrabbit==0.2.1
 cwlformat
 packaging
\ No newline at end of file
diff --git a/sbpack/noncwl/nextflow.py b/sbpack/noncwl/nextflow.py
index f52950b..b581ae8 100755
--- a/sbpack/noncwl/nextflow.py
+++ b/sbpack/noncwl/nextflow.py
@@ -46,6 +46,9 @@ def nf_schema_build(self):
         Build nextflow schema using nf_core schema build feature and save to
         a file
         """
+        if self.nf_schema_path:
+            return
+
         nf_schema_path = os.path.join(
             self.workflow_path,
             NF_SCHEMA_DEFAULT_NAME,
@@ -64,6 +67,8 @@ def nf_schema_build(self):
         )
         self.nf_schema_path = nf_schema_path
 
+        self.init_config_files()
+
 
 def main():
     # CLI parameters
@@ -248,13 +253,6 @@ def main():
             schema = yaml.safe_load(s)
             nf_wrapper.sb_wrapper.load(schema)
     else:
-        # build schema
-        # Do this only if the nextflow_schema.json is missing
-        if not nf_wrapper.nf_schema_path:
-            nf_wrapper.nf_schema_build()
-            # update the nextflow_schema.json location
-            nf_wrapper.init_config_files()
-
         # Create app
         nf_wrapper.generate_sb_app(
             execution_mode=execution_mode,

From cbfeeec32bd59e83f2f9813079cde1387a897286 Mon Sep 17 00:00:00 2001
From: pavlemarinkovic <pavle.marinkovic@sbgenomics.com>
Date: Thu, 11 Jul 2024 17:28:03 +0200
Subject: [PATCH 3/4] Use wrabbit 0.2.1

---
 sbpack/pack.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/sbpack/pack.py b/sbpack/pack.py
index 17195e2..5563a88 100755
--- a/sbpack/pack.py
+++ b/sbpack/pack.py
@@ -246,6 +246,15 @@ def resolve_steps(
                     cwl["cwlVersion"] = v["run"]["cwlVersion"]
                     # not really enough, but hope for the best
 
+                if 'sbg:appVersion' not in v["run"]:
+                    v["run"]['sbg:appVersion'] = [cwl.get(
+                        "cwlVersion", cwl_version)]
+                else:
+                    version_ = cwl.get(
+                        "cwlVersion", cwl_version)
+                    if version_ not in v["run"]['sbg:appVersion']:
+                        v["run"]['sbg:appVersion'].append(version_)
+
     return cwl
 
 

From 3481fd8ae21fb217a3f323af0be9633da4b385cb Mon Sep 17 00:00:00 2001
From: pavlemarinkovic <pavle.marinkovic@sbgenomics.com>
Date: Thu, 11 Jul 2024 17:29:15 +0200
Subject: [PATCH 4/4] Use wrabbit 0.2.1

---
 sbpack/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sbpack/version.py b/sbpack/version.py
index abb3831..0047d7f 100755
--- a/sbpack/version.py
+++ b/sbpack/version.py
@@ -1 +1 @@
-__version__ = "2024.6.24rc1"
+__version__ = "2024.7.11rc1"